Welcome to pykinetic's Documentation!

Pykinetic is a project that aims to facilitate the automation and generation of kinetic and microkinetic models. Pykinetic acts as an intermediate layer between the user and the mathematical model that is then simulated to obtain the kinetic data. This functionality can be done either through the use of the pykinetic python library or through the use of the command line apps: "pykinetic-model.py" and "pykinetic-scan.py". The minimal source code to run the simulation is the output of pykinetic and currently python and c++ are supported. Compiling and executing that code leads to the simulation of the chemical system.

Getting Started

• Installation
  • Prerequisites
  • Installing the dependencies
  • Installing pykinetic
  • Running the tests
  • Uninstalling pykinetic
• File Formats
  • Compounds File
    • General format:
    • Compound label rules:
    • Compounds file example:
  • Reactions File
    • General format:
    • Symbols:
    • Reactions file example:
  • Simulation Parameters File
• Writers
  • Python
  • C++

Examples

• Scripts Usage
  • pykinetic-model.py
  • pykinetic-scan.py
• Library Usage
  • Creating a model from scratch
  • Modifying and loading a model
• Workflows

Python API

• pykinetic
  • classes
    • Energy
    • ChemicalSystem
    • Compound
    • Reaction
    • Transition states
    • Parameters
    • MassBalance
    • JacobianElement
  • writers
    • base
      • Writer
    • python
      • Batch
      • PFR
      • SemiBatch
      • SemiBatchExtended
    • C++
      • Batch
  • utils
    • Pykinetic Utilities
    • Specialized ChemicalSystems
  • userinput

About

• Developers
• Citation
• Contribution

License

pykinetic is freely available under an MIT License

Indices and tables

• Index

• Module Index

• Search Page